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mmu_circClk4_388
Basic information of circular RNA
PanCircBase ID:
mmu_circClk4_388
mm39_Chr. Position ID:
chr11|51166596|51171264|+
Gene name:
Clk4
Transcript:
ENSMUST00000093132.13
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
8,9,10,11
Exon/intron offsets:
0,348,2083,4588
Genomic length:
4668
Exon/intron sizes in nt:
95,130,83,80
Flanking exon/introns:
chr11:51166405-51166596|chr11:51171264-51171935
Splice length:
388
Other database IDs:
circBase: hsa_circ_0128686, circAtlas: hsa-SCAF8_0001, CIRCpedia: HSA_CIRCpedia_51330
Human Ortholog IDs:
Mature spliced Sequence:
TTTTACATCATAATAAATTAACACACACGGACCTAAAACCTGAAAATATTTTATTTGTGAAGTCTGACTATGTAGTCAAATACAATTCTAAAATGAAACGAGATGAGCGCACATTGAAAAACACAGATATCAAAGTTGTTGATTTTGGAAGTGCAACATATGACGACGAACATCATAGTACTTTGGTGTCCACAAGGCACTACAGGGCTCCAGAGGTCATTTTGGCTCTAGGTTGGTCTCAGCCTTGTGATGTTTGGAGCATAGGCTGCATTCTTATTGAGTACTACCTTGGGTTCACAGTCTTTCAGACCCACGATAGTAAAGAGCACCTGGCAATGATGGAGCGGATCTTAGGACCCATCCCAGCACATATGATCCAGAAGACAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
TGGGTTCACAGTCTTTCAGACC
60.16
AGGTTTTAGGTCCGTGTGTGT
59.51
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
GGTTCACAGTCTTTCAGACCCA
60.16
TCAGGTTTTAGGTCCGTGTGT
59.24
140
PCR template sequence:
TTGGGTTCACAGTCTTTCAGACCCACGATAGTAAAGAGCACCTGGCAATGATGGAGCGGATCTTAGGACCCATCCCAGCACATATGATCCAGAAGACAAGTTTTACATCATAATAAATTAACACACACGGACCTAAAACCTGAAAATATTTTATTTGTGAAGTCTGACTATGTAGTCAAATACAATTCTAAAATGAAACG
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
NA
Interacting miRNAs (#binding sites)
NA
siRNAs for circular RNA silencing
Junction sequence
TCCAGAAGACAAGTTTTACATCATAA
siRNA sets
TTATGATGTAAAACTTGTC, TATGATGTAAAACTTGTCT, ATGTAAAACTTGTCTTCTG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCCLK4_388_ORF_1
0.7401
0.09670306
0.221020119
309
ORF sequence:
ATGAAACGAGATGAGCGCACATTGAAAAACACAGATATCAAAGTTGTTGATTTTGGAAGTGCAACATATGACGACGAACATCATAGTACTTTGGTGTCCACAAGGCACTACAGGGCTCCAGAGGTCATTTTGGCTCTAGGTTGGTCTCAGCCTTGTGATGTTTGGAGCATAGGCTGCATTCTTATTGAGTACTACCTTGGGTTCACAGTCTTTCAGACCCACGATAGTAAAGAGCACCTGGCAATGATGGAGCGGATCTTAGGACCCATCCCAGCACATATGATCCAGAAGACAAGTTTTACATCATAA
Peptide sequence:
MKRDERTLKNTDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFQTHDSKEHLAMMERILGPIPAHMIQKTSFTS
IRESfinder result
IRESfinder score
0.627274905
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
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